@@ -120,16 +115,16 @@ Next, we can analyze the specific characteristics of both the target molecule an
**How it was implemented:**
To execute the program via the command-line interface, navigate to the directory where the md file is located. Once in the directory, users can run one of the following commands:
To execute the program via the command-line interface, navigate to the directory where the md file is located. Once in the directory, users can run one of the following commands. Please ensure that the file or folder path provided is the complete path to the selected file or folder.
./md --addMolecule [FILE PATH]: This command adds the molecule specified in the file path to the database. For example, to add biotin from the file biotin.txt to the database, run: ./md --addMolecule /path/to/directory/biotin.txt.
./md --addBulk [FOLDER PATH]: This command allows users to add multiple molecules in bulk from a specified folder. For example, to add all molecules inside the Molecules folder, simply run: ./md --addBulk path/to/Molecules.
./md --delete [FILE PATH]: This command deletes the molecule specified in the file path to the database. For example, to delete biotin from the file biotin.txt, run:./md --delete /path/to/directory/biotin.txt
./md --findMolecule [FILE PATH]: This command searches for the isomorphic molecule specified in the file path within the database. For instance, to find an isomorphic molecule to biotin within the database using the file biotin.txt, run: ./md --findMolecule /path/to/directory/biotin.txt. If the program finds an exact match, it will display “FOUND.” If not, it will show “NO EXACT MATCH FOUND” and return the most similar molecule to the given molecule within the database.
./md --addProteins [FILE PATH]: This command adds protein molecules generated by `--makeManySimple` command and `--makeFewComplex` command to the database. The default path for --makeManySimple is “../simple” and `--makeFewComplex` “../complex”. For instance, ./md --addproteins ../simple and ./md --addProteins ../complex.
./md --findSubgraph [FILE PATH]: This command finds and outputs all molecules containing a subgraph provided in the file path. If no subgraph is found, the program outputs "No subgraph found."
./md --downloadPubChem start,end: This command downloads molecules from the PubChem database. "start" and "end" are indices or Compound ID (CID) numbers of the molecules in the PubChem database. For example, to download molecules 20-27, type: ./md --downloadPubChem 20,27
@@ -142,9 +137,11 @@ To execute the program via the command-line interface, navigate to the directory
./md --printName: This command prints the name of the database.
./md --makeManySimple: This command generates 10 million molecule files with between 52 and 136 atoms.
./md --makeManySimple: This command generates 10 million molecule files, each having between 52 and 136 atoms. Generated molecules are saved in a folder called `simple` which is located in the parent directory of the project folder. Users do not need to specify a file or folder path for this feature.
./md --makeFewComplex: This command generates 10,000 million molecule files with over 10,000 atoms each.
./md --makeFewComplex: This command creates 10,000 million molecule files, each with over 10,000 atoms. Generated molecules are saved in a folder called `complex` that is located in the parent directory of the project folder. Users do not need to specify a file or folder path for this feature.
./md --addProteins [FILE PATH]: This command adds proteins created by the `--makeManySimple` and `--makeFewComplex` commands. Please make sure to select a file path, which is either the Complex or Simple directory.
./md --marco: This command pings the server to check if it is still alive.
@@ -152,7 +149,6 @@ The Main.java class, which facilitates the command-line interface, also includes
Accepted feedback: Changes that were proposed in peer review and they you ended up adopting, together with a brief explanation why you chose to accept them.
**Change 0:**
Previously, the file chooser always opened the home folder instead of the last accessed folder. We updated the file chooser to remember the previously selected folder, allowing users to revisit it without needing to navigate again. We acknowledged this feedback as navigating to a working directory each time users reselected a file could be cumbersome.
**Change 1:**
We implemented a user-friendly terminal output message when the GUI encounters a molecule not found in the PubChem database or misspelled, rather than displaying the entire stack trace. We incorporated this feedback to provide users with simpler error messages.
**Change 2:**
One student suggested adding a feature allowing users to add multiple molecules from a specified directory. We agreed with this suggestion as it would enhance convenience compared to adding molecules one file at a time. As a result, we introduced a new command/button that enables users to specify a folder, prompting the program to add all molecules within that folder to the database.
**Change 3:**
Multiple students noted that downloadPubChem was not working, which came as an oversight due to the Lab Computer’s default outdated version of Python (2.7.5). Since the function relies on a script that requires Python3, it did not run correctly without updating the Python version. This functionality is restored via the command $ module load anaconda/3, which loads Python 3.7.10. Additionally, this module comes with networkx installed, therefore removing the pip install requirement.
**Change 4**
One student suggested adding a delete feature to our database so that a user can remove duplicates or any other unwanted molecules. We agreed that this is an obvious feature that our database should have and as a result we implemented a delete button to our GUI and a delete function to the command line interface. A user needs to specify a file path to an unwanted molecule file and then will have the ability to remove that molecule from the database.
Rejected feedback: Changes that were proposed in peer review and they you ended up not adopting, together with a brief explanation why you chose to reject them.
**Change 0:**
One reviewer suggested simplifying the search process by requesting only the molecule name instead of the entire file path to the molecule text file. They proposed implementing backend functionality to automatically retrieve the text file from the Molecules directory. We are hesitant to implement this feedback because we want users to have the flexibility to add molecule files from any location on the machine.
**Change 1:**
One comment mentioned that the `--makeManySimple` command takes too long to generate the protein files on lab computers. Optimizing the command is not a high priority, and there is very little that can be done to make the lab computers run faster. Therefore, the comment is rejected.
Other changes: Changes that you implemented, but were not mentioned in peer review, together with a brief explanation for why you implemented them.
**Change 0:**
We revised our INSTALL.txt and README.md to improve clarity and understanding.
**Change 1:**
After testing with an extensive variety of molecules, we identified that --findMolecule misrepresented two molecules as equal, so we improved the comparison logic to perform a more extensive search. The test cases labeled TestSame1.txt and TestSame2.txt have identical atoms, but the order of connection is different. Our database should detect this. This is currently an unimplemented feature under the branch “improve-isomorphism”.
**Change 2:**
We have incorporated GUI buttons for "Make Simple Molecules," "Make Complex Molecules," and "Add Proteins." These buttons enable users to execute the respective functionalities previously exclusive to the command line interface.
**Change 3:**
A dedicated branch, “23-database-partition”, is created for implementing a partitioned database. The purpose is to solve the out-of-memory error caused by adding a very large number of molecules and/or very complex molecules. It features partitioning by the ratio of Carbon and Hydrogen atoms to all atoms in the molecule, and keeping a number of partitions in the memory and swapping out old ones as needed.
